GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Stenotrophomonas chelatiphaga DSM 21508

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_057507564.1 ABB28_RS04920 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-15108
         (486 letters)



>NCBI__GCF_001431535.1:WP_057507564.1
          Length = 501

 Score =  225 bits (574), Expect = 2e-63
 Identities = 147/440 (33%), Positives = 225/440 (51%), Gaps = 20/440 (4%)

Query: 15  IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANERI 74
           IDG+F+ S      D +NPAT++ L  V     +E+D AV AAK+A    W+K     R 
Sbjct: 12  IDGQFIESSTAHWQDVVNPATQDVLAQVPFATTSEVDDAVAAAKEAFK-TWRKTPIGTRA 70

Query: 75  AVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEATQ 134
            +  K   LI E   EL+   S + GK T      D+ R         ++   I N   Q
Sbjct: 71  RIFLKYQQLIRENMSELAHTLSAEQGK-TVPDAEGDVFRGLE----VVEHAAAIGN--LQ 123

Query: 135 MDDVALN-------YAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTP 187
           + ++A N       Y + +P+GV   I P+N P ++  W    A+A GNT V+KP+E  P
Sbjct: 124 LGELANNVANGVDTYTLMQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDP 183

Query: 188 MTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASA 247
           M    L E+  +AG+P GV+N+VH  G      A+ +HPD+ A+SF G T  G  +   A
Sbjct: 184 MVTMRLVELALEAGIPKGVLNVVH--GGEEVVNAICDHPDIKAVSFVGSTRVGTHVYNRA 241

Query: 248 AKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAF 307
           +   KR+   +G KN  V+  D+N ++ +   + ++F   G+ C+  S + +   A  ++
Sbjct: 242 SLAGKRVQCMMGAKNHAVVLPDANKEQTLNAMVGAAFGAAGQRCMAASTLVLVGEA-RSW 300

Query: 308 LEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRP--EG 365
           +   VAK K L V     A T VG +IS    ERV G I   +E+G T+   G+ P  +G
Sbjct: 301 VPDLVAKAKTLKVSAGSVAGTDVGPVISCSARERVEGLIASGLEQGATLDLDGRNPQVDG 360

Query: 366 LEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTN 425
            EKG F+ PTI +G+T D R+ +EEIFGPV+ ++  +T E+ +  +N    G   +V+T 
Sbjct: 361 FEKGNFVGPTIFSGVTTDMRIYQEEIFGPVLVILEAETLEDAIALVNSNPNGNGTAVFTQ 420

Query: 426 DLRRAHRVAGQIEAGIVWVN 445
               A +    I+ G V +N
Sbjct: 421 SGAAARKFQEDIDVGQVGIN 440


Lambda     K      H
   0.318    0.136    0.404 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 545
Number of extensions: 30
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 486
Length of database: 501
Length adjustment: 34
Effective length of query: 452
Effective length of database: 467
Effective search space:   211084
Effective search space used:   211084
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory